Influenza Research Database - Revision history

Ebachour: issues with powerpoint, switched to pdf, plz don't mark off

2017-10-05T07:03:22Z

issues with powerpoint, switched to pdf, plz don't mark off

Ebachour at 07:00, 5 October 2017

2017-10-05T07:00:02Z

Ebachour: Fixing last things

2017-10-05T06:58:58Z

Fixing last things

Emmatyrnauer: /* Electronic notebook */ added typo check

2017-10-05T06:07:23Z

‎Electronic notebook: added typo check

Emmatyrnauer: /* Upkeep */ adding period

2017-10-05T06:03:22Z

‎Upkeep: adding period

Emmatyrnauer: adding category journal entry

2017-10-05T05:59:43Z

adding category journal entry

Emmatyrnauer: /* Content */ data tense error fix

2017-10-05T05:56:41Z

‎Content: data tense error fix

Emmatyrnauer: /* Powerpoint Presentation */ switching to lowercase

2017-10-05T05:43:10Z

‎Powerpoint Presentation: switching to lowercase

Emmatyrnauer: adding powerpoint presentation heading

2017-10-05T05:42:44Z

adding powerpoint presentation heading

Emmatyrnauer: /* Electronic notebook */ adding to electronic notebook

2017-10-05T05:41:56Z

‎Electronic notebook: adding to electronic notebook

@@ Line 89: / Line 89: @@
 =Powerpoint presentation=
-[[File:emma_and_eddie_powerpoint_IRD.pptx | Our Powerpoint for IRD]]
+[[File:EDDIE_EMMA_PWPT.pdf | Our Powerpoint for IRD]]
 =Electronic notebook=

@@ Line 73: / Line 73: @@
 # For the most part everything is clearly labeled and organized well. They have five main sections right under their logo which help direct you to the part of the site that you are looking for. The dropdown menus under each of these sections has labels that aren't confusing, and therefore take you to exactly the part of the site that you think you are going to.
 ==Help Sections==
-#: One of the five main sections is labeled help (easily spotted and right at the top-center of the page) and has the following sub-sections:
+# One of the five main sections is labeled help (easily spotted and right at the top-center of the page) and has the following sub-sections:
 ## Help Manual
 ## Tutorials & Training Materials
@@ Line 89: / Line 89: @@
 =Powerpoint presentation=
-[[emma_and_eddie_powerpoint_IRD.pptx | Our Powerpoint for IRD]]
+[[File:emma_and_eddie_powerpoint_IRD.pptx | Our Powerpoint for IRD]]
 =Electronic notebook=

@@ Line 35: / Line 35: @@
 =General utility of the database to the scientific community=
-# Are there links to other databases?  Which ones?
+==Where does the data come from?==
-#:: Although most of the data is generated by the IRD team, the database also imports data from the following databases:
+#Although most of the data is generated by the IRD team, the database also imports data from the following databases:
-#::* [https://www.ncbi.nlm.nih.gov/genbank/ NCBI - GenBank]
+#* [https://www.ncbi.nlm.nih.gov/genbank/ NCBI - GenBank]
-#::* [https://www.ncbi.nlm.nih.gov/refseq/ NCBI - RefSeq
+#* [https://www.ncbi.nlm.nih.gov/refseq/ NCBI - RefSeq
-#::* [http://www.iedb.org/ Immune Epitope Database (IEDB)]
+#* [http://www.iedb.org/ Immune Epitope Database (IEDB)]
-#::* [http://www.uniprot.org/ UniProt]
+#* [http://www.uniprot.org/ UniProt]
-#::* [http://www.rcsb.org/pdb/home/home.do RCSB Protein Data Bank (PDB)]
+#* [http://www.rcsb.org/pdb/home/home.do RCSB Protein Data Bank (PDB)]
-#::* [https://www.ebi.ac.uk/thornton-srv/databases/CSA/ Catalytic Site Atlas]
+#* [https://www.ebi.ac.uk/thornton-srv/databases/CSA/ Catalytic Site Atlas]
-#::* [http://avibase.bsc-eoc.org/avibase.jsp?lang=EN Avibase]
+#* [http://avibase.bsc-eoc.org/avibase.jsp?lang=EN Avibase]
-# Is it convenient to browse the data?
+==Searching the database==
-#:: IRD has multiple ways to browse and search the data within their database. They also have a number of tools that make it convenient to refine and analyze the search as well as save the data you are working on to your "workbench" so you can come back to it later.
+# IRD has multiple ways to browse and search the data within their database. They also have a number of tools that make it convenient to refine and analyze the search as well as save the data you are working on to your "workbench" so you can come back to it later.
-#::# You can use their quick search tool, to "search for sequence records using any text terms in key text fields and public IDs (e.g. accession numbers) of nucleotide and protein sequence records, strain data, surveillance data, and human clinical metadata."
+## You can use their quick search tool, to "search for sequence records using any text terms in key text fields and public IDs (e.g. accession numbers) of nucleotide and protein sequence records, strain data, surveillance data, and human clinical metadata."
-#::# Or, you search using any of the following, focused, search tools:
+## Or, you search using any of the following, focused, search tools:
-#::#* Sequences & Strains
+##* Sequences & Strains
-#::#* Animal Surveillance
+##* Animal Surveillance
-#::#* 3D Protein Structure Files
+##* 3D Protein Structure Files
-#::#* Human Clinical Metadata
+##* Human Clinical Metadata
-#::#* Serology Experiments (Beta)
+##* Serology Experiments (Beta)
-#::#* Host Factor Data
+##* Host Factor Data
-#::#* Antiviral Drugs
+##* Antiviral Drugs
-#::#* Immune Epitopes
+##* Immune Epitopes
-#::#* Phenotypes
+##* Phenotypes
-#::#* PCR Primer Probe Data
+##* PCR Primer Probe Data
-#::#* Sequence Feature Variant Types
+##* Sequence Feature Variant Types
-#::#* Human Clinical Studies and Lab Experiments (Beta)
+##* Human Clinical Studies and Lab Experiments (Beta)
-#:: With all of these tools, you have many options to access any single piece of data. This provides a lot of convenience when it comes too trying to locate anything within their database.
+==Exporting the Data==
-# Is it convenient to download the data?
+# With all of these tools, you have many options to access any single piece of data. This provides a lot of convenience when it comes too trying to locate anything within their database.
-#:: Yes, once you've used one of their various search tools to find the data point that you need, you can download the data into one of the following formats:
+# Once you've used one of their various search tools to find the data point that you need, you can download the data into one of the following formats:
-#::# GFF3
+## GFF3
-#::# Segment FASTA
+## Segment FASTA
-#::# Gene FASTA
+## Gene FASTA
-#::# CDS FASTA
+## CDS FASTA
-#::# Protein FASTA
+## Protein FASTA
-#* In what file formats are the data provided?
+# All file formats that they provide are standard in bioinformatics.
-#:: Listed above.
+==User-friendliness & Organization==
-#* Are they standard or non-standard formats?
+# It is a pretty user-friendly database. They have done a good job making all of their search and download tools very obvious and easy to use. Obviously is someone who has no biological background would have a hard time searching data, but that doesn't make the site not user-friendly.
-#:: All file formats that they provide are standard in bioinformatics.
+# For the most part everything is clearly labeled and organized well. They have five main sections right under their logo which help direct you to the part of the site that you are looking for. The dropdown menus under each of these sections has labels that aren't confusing, and therefore take you to exactly the part of the site that you think you are going to.
-# Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
+==Help Sections==
-#:: It is a pretty user-friendly database. They have done a good job making all of their search and download tools very obvious and easy to use. Obviously is someone who has no biological background would have a hard time searching data, but that doesn't make the site not user-friendly.
+#: One of the five main sections is labeled help (easily spotted and right at the top-center of the page) and has the following sub-sections:
-#* Is the website well-organized?
+## Help Manual
-#:: For the most part everything is clearly labeled and organized well. They have five main sections right under their logo which help direct you to the part of the site that you are looking for. The dropdown menus under each of these sections has labels that aren't confusing, and therefore take you to exactly the part of the site that you think you are going to.
+## Tutorials & Training Materials
-#* Does it have a help section or tutorial?
+## Frequently Asked Questions
-#:: Yes, one of the five main sections is labeled help (easily spotted and right at the top-center of the page) and has the following sub-sections:
+## IRD Computational Protocols
-#::# Help Manual
+## IRD Glossary
-#::# Tutorials & Training Materials
+## Contact Us
-#::# Frequently Asked Questions
+## Cite IRD
-#::# IRD Computational Protocols
+# Their help manual is very extensive with detailed written instructions on how to access/use any part of the site. Their Tutorials and Training Materials page is also very helpful because it provides links to video instructions on how to do the most used tasks within IRD.
 =Summary judgment=
-# Would you direct a colleague unfamiliar with the field to use it?
+# Influenza Research Database is good for any biologist that is either new to bioinformatics or has veteran status in the field
-# Is this a professional or hobby database?
+# It is a very well-organized site that congregates its own data with the data of most of the big name bio-databases
 =Powerpoint presentation=
 =Electronic notebook=
@@ Line 105: / Line 99: @@
 #While we worked with the people noted above, this journal entry was completed by Emma and Eddie and not copied from another source.
 [[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 16:48, 4 October 2017 (PDT)
 =References=

@@ Line 98: / Line 98: @@
 =Electronic notebook=
-For this assignment, we chose the Influenza Research Database after class and did individual research on it. We then met up in the library and began working on the database's wiki page. First, we titled the page "Influenza Research database" and linked both of our user pages to this page. We then made an outline with individual headings corresponding to each of the main sections (this allowed us to work on the wiki at the same time by just being able to edit individual sections).  We read the corresponding paper in NAR to get a general background for usage of the database and then began exploring the database itself. Emma worked on the first two sections (general information and scientific quality) while Eddie focused on the final one (general utility of the database to the scientific community). We went down the list of questions navigating through the paper and database to find the answers. Information was gathered by clicking on different tabs in the database and randomly browsing/exploring. Once we finished our individual sections for the analysis of the database, we started constructing our powerpoint presentation on google slides. We used the same basic format and layout in our powerpoint as we did in our wiki page and followed the presentation and powerpoint guidelines that were gone over in class. Once we finished our powerpoint, we uploaded the presentation to the wiki page.
+For this assignment, we chose the Influenza Research Database after class and did individual research on it. We then met up in the library and began working on the database's wiki page. First, we titled the page "Influenza Research database" and linked both of our user pages to this page. We then made an outline with individual headings corresponding to each of the main sections (this allowed us to work on the wiki at the same time by just being able to edit individual sections).  We read the corresponding paper in NAR to get a general background for usage of the database and then began exploring the database itself. Emma worked on the first two sections (general information and scientific quality) while Eddie focused on the final one (general utility of the database to the scientific community). We went down the list of questions navigating through the paper and database to find the answers. Information was gathered by clicking on different tabs in the database and randomly browsing/exploring. Once we finished our individual sections for the analysis of the database, we started constructing our powerpoint presentation on google slides. We used the same basic format and layout in our powerpoint as we did in our wiki page and followed the presentation and powerpoint guidelines that were gone over in class. Once we finished our powerpoint, we checked for typos and uploaded the presentation to the wiki page.
 =Acknowledgements=

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 ===Upkeep===
 *It is unclear when the database was first released online. However, its most distant publication was in 2006 ([https://www.fludb.org/brc/publicationsIRD.spg?method=pubsPres&decorator=influenza IRD Resource Publications and Presentations]).
-*While sequences are downloaded from GenBank, curated, and added to the IRD database daily, updates to generated and imported public data are made less often. The most recent updates for this information occurred between May 2017 and October 2017 ([https://www.fludb.org/brc/dataUpdates.spg?decorator=influenza IRD Data Updates])
+*While sequences are downloaded from GenBank, curated, and added to the IRD database daily, updates to generated and imported public data are made less often. The most recent updates for this information occurred between May 2017 and October 2017 ([https://www.fludb.org/brc/dataUpdates.spg?decorator=influenza IRD Data Updates]).
 =General utility of the database to the scientific community=

← Older revision		Revision as of 05:59, 5 October 2017
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	#Influenza Research Database: update 2017. Retrieved October 4, 2017, from https://www.fludb.org/brc/home.spg?decorator=influenza.		#Influenza Research Database: update 2017. Retrieved October 4, 2017, from https://www.fludb.org/brc/home.spg?decorator=influenza.
	# Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, Sanjeev Kumar, Christopher N. Larsen, Alexandra J. Lee, Xiaomei Li, Catherine Macken, Colin Mahaffey, Brett E. Pickett, Brian Reardon, Thomas Smith, Lucy Stewart, Christian Suloway, Guangyu Sun, Lei Tong, Amy L. Vincent, Bryan Walters, Sam Zaremba, Hongtao Zhao, Liwei Zhou, Christian Zmasek, Edward B. Klem, Richard H. Scheuermann; Influenza Research Database: An integrated bioinformatics resource for influenza virus research, Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D466–D474. Retrieved October 4, 2017 from https://doi.org/10.1093/nar/gkw857.		# Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, Sanjeev Kumar, Christopher N. Larsen, Alexandra J. Lee, Xiaomei Li, Catherine Macken, Colin Mahaffey, Brett E. Pickett, Brian Reardon, Thomas Smith, Lucy Stewart, Christian Suloway, Guangyu Sun, Lei Tong, Amy L. Vincent, Bryan Walters, Sam Zaremba, Hongtao Zhao, Liwei Zhou, Christian Zmasek, Edward B. Klem, Richard H. Scheuermann; Influenza Research Database: An integrated bioinformatics resource for influenza virus research, Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D466–D474. Retrieved October 4, 2017 from https://doi.org/10.1093/nar/gkw857.
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		+	[[Category:Journal Entry]]

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 **Personal workbench (data storage and sharing)
 *IRD contains avian and non-human mammalian influenza surveillance data, human clinical data associated with virus extracts, phenotypic characteristics of viruses isolated from extracts, and all genomic and proteomic data available in public repositories for influenza viruses ([https://www.fludb.org/brc/staticContent.spg?decorator=influenza&type=FluInfo&subtype=Mission Mission]).
-*It includes both primary and secondary data that appears to be both electronically curated and manually curated in-house. On the [https://www.fludb.org/brc/dataSources.spg?decorator=influenza Data Sources] page it mentions that it uses algorithms to generate different data types. In the [https://academic.oup.com/nar/article/45/D1/D466/2770652/Influenza-Research-Database-An-integrated?searchresult=1 NAR paper] authors also mention that some of the data is integrated from IRD in-house curation and annotation pipelines.
+*It includes both primary and secondary data that appear to be both electronically curated and manually curated in-house. On the [https://www.fludb.org/brc/dataSources.spg?decorator=influenza Data Sources] page it mentions that it uses algorithms to generate different data types. In the [https://academic.oup.com/nar/article/45/D1/D466/2770652/Influenza-Research-Database-An-integrated?searchresult=1 NAR paper] authors also mention that some of the data are integrated from IRD in-house curation and annotation pipelines.
 ===Maintenance===